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Acta Crystallogr Sect E Struct Rep Online. 2009 December 1; 65(Pt 12): o2994.
Published online 2009 November 4. doi:  10.1107/S1600536809045140
PMCID: PMC2971978

6-Benzyl­sulfanyl-9H-purine

Abstract

The phenyl ring of the title compound, C12H10N4S, a purine derivative, is oriented at a dihedral angle of 76.65 (6)° with respect to the purine ring system. An inter­molecular N—H(...)N hydrogen bonds stabilizes the crystal structure.

Related literature

For the biological activity of purine derivatives, see: Lepage et al. (1964 [triangle]); Mitsuya & Border (1986 [triangle]); Ragazzi et al. (1989 [triangle]).

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Object name is e-65-o2994-scheme1.jpg

Experimental

Crystal data

  • C12H10N4S
  • M r = 242.30
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2994-efi1.jpg
  • a = 5.5717 (3) Å
  • b = 9.4733 (4) Å
  • c = 22.4656 (14) Å
  • V = 1185.79 (11) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.26 mm−1
  • T = 296 K
  • 0.29 × 0.12 × 0.09 mm

Data collection

  • Bruker Kappa APEXII CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2007 [triangle]) T min = 0.930, T max = 0.978
  • 7941 measured reflections
  • 2941 independent reflections
  • 2102 reflections with I > 2σ(I)
  • R int = 0.032

Refinement

  • R[F 2 > 2σ(F 2)] = 0.040
  • wR(F 2) = 0.088
  • S = 0.98
  • 2941 reflections
  • 157 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.17 e Å−3
  • Δρmin = −0.17 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1207 Friedel pairs
  • Flack parameter: −0.09 (8)

Data collection: APEX2 (Bruker, 2007 [triangle]); cell refinement: SAINT (Bruker, 2007 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]) and PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]) and PLATON.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809045140/bt5117sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809045140/bt5117Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

IF acknowledges the Higher Education Commission, Pakistan for providing funding for this research.

supplementary crystallographic information

Comment

The synthesis of purine derivatives has received considerable attention on account of their biological activity especially as antitumor (Lepage et al., 1964), anti HTVL (Mitsuya & Border, 1986) and anti asthmatic (Ragazzi et al., 1989) agents. During our search to find new synthetic antithyroid agents, certain purine derivatives were prepared. 6-(benzylthio)-7H-purine was synthesized during such an effort. The compound is now under study for possible antithyroid activity.

The phenyl ring is oriented at adihedral angle of 76.65 (6) ° with respect to purine ring system. An intermolecular N–H···N hydrogen bonds stabilizes the crystal structure.

Experimental

To a solution of 6-mercaptopurine (0.171 g) 1 mmol in 2 N NaOH (10 ml), benzyl bromide 1 mmol (0.171 g) was added and stirred at room temperature for 30 minutes. The pH of the mixture was adjusted at 5 with glacial acetic acid and the precipitates were collected, washed with water and diethyl ether. The crystals suitable for X-ray diffraction were grown in dichloromethane by slow evaporation at room temperature.

Refinement

The H-atoms bonded to C were refined geometrically and treated as riding atoms with Caromatic—H = 0.93Å and Cmethylene—H = 0.97Å and Uiso(H) = 1.2Ueq(C). The N–H atom was refined at calculated position with N–H=0.894 (19) Uiso(H) = 1.2Ueq (parent N-atom)

Figures

Fig. 1.
The crystal structure diagram of the title compound duly labeled with 50% probability level of drawn thermal ellipsoids.
Fig. 2.
Unit cell diagram showing the intermolecular hydrogen bonding using dashed lines. The hydrogen atoms not involved in hydrogen bonding have been omitted for clarity.

Crystal data

C12H10N4SF(000) = 504
Mr = 242.30Dx = 1.357 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 2230 reflections
a = 5.5717 (3) Åθ = 2.3–24.8°
b = 9.4733 (4) ŵ = 0.26 mm1
c = 22.4656 (14) ÅT = 296 K
V = 1185.79 (11) Å3Needle, red
Z = 40.29 × 0.12 × 0.09 mm

Data collection

Bruker Kappa APEXII CCD diffractometer2941 independent reflections
Radiation source: fine-focus sealed tube2102 reflections with I > 2σ(I)
graphiteRint = 0.032
[var phi] and ω scansθmax = 28.3°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2007)h = −7→6
Tmin = 0.930, Tmax = 0.978k = −12→12
7941 measured reflectionsl = −28→29

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.040H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.088w = 1/[σ2(Fo2) + (0.0419P)2] where P = (Fo2 + 2Fc2)/3
S = 0.98(Δ/σ)max < 0.001
2941 reflectionsΔρmax = 0.17 e Å3
157 parametersΔρmin = −0.16 e Å3
0 restraintsAbsolute structure: Flack (1983), 1207 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: −0.09 (8)

Special details

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'s involving l.s. planes.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > 2σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
S10.47086 (11)0.20744 (5)0.15044 (2)0.05534 (18)
N10.3943 (4)−0.07206 (16)0.13660 (7)0.0553 (5)
N20.6348 (4)−0.25776 (16)0.18001 (8)0.0577 (5)
N30.9619 (4)−0.16476 (15)0.23955 (8)0.0519 (5)
H3N1.020 (4)−0.2456 (19)0.2541 (8)0.062*
N40.8929 (3)0.06585 (15)0.22833 (7)0.0488 (4)
C10.7639 (4)−0.15403 (16)0.20432 (9)0.0454 (5)
C20.7219 (4)−0.01004 (17)0.19749 (8)0.0432 (5)
C30.5298 (4)0.02806 (17)0.16181 (8)0.0447 (5)
C40.4558 (4)−0.2074 (2)0.14777 (10)0.0618 (6)
H40.3578−0.27500.13020.074*
C51.0294 (4)−0.03046 (17)0.25248 (10)0.0530 (5)
H51.1608−0.00900.27640.064*
C60.2345 (4)0.2002 (2)0.09542 (10)0.0662 (6)
H6A0.27630.13280.06460.079*
H6B0.08620.16940.11400.079*
C70.2003 (4)0.3442 (2)0.06836 (9)0.0500 (5)
C80.3547 (5)0.3944 (2)0.02616 (10)0.0646 (6)
H80.48830.34090.01580.077*
C90.3174 (5)0.5222 (2)−0.00144 (11)0.0741 (8)
H90.42280.5532−0.03070.089*
C100.1270 (6)0.6027 (2)0.01415 (12)0.0708 (7)
H100.10110.6889−0.00460.085*
C11−0.0261 (5)0.5576 (3)0.05709 (12)0.0780 (7)
H11−0.15500.61390.06840.094*
C120.0092 (5)0.4280 (3)0.08406 (10)0.0690 (6)
H12−0.09760.39720.11310.083*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0640 (4)0.0405 (3)0.0616 (3)−0.0021 (3)−0.0128 (3)0.0078 (2)
N10.0659 (12)0.0470 (9)0.0530 (11)−0.0109 (9)−0.0074 (9)0.0019 (8)
N20.0708 (12)0.0373 (8)0.0650 (12)−0.0098 (9)−0.0048 (11)−0.0040 (8)
N30.0602 (12)0.0309 (7)0.0647 (11)0.0005 (8)−0.0058 (10)0.0064 (7)
N40.0571 (11)0.0330 (7)0.0562 (11)−0.0034 (8)−0.0085 (9)0.0020 (7)
C10.0582 (14)0.0303 (9)0.0478 (11)−0.0028 (9)0.0053 (10)0.0011 (8)
C20.0525 (13)0.0308 (9)0.0464 (11)−0.0040 (9)0.0029 (9)0.0022 (8)
C30.0526 (12)0.0386 (9)0.0431 (11)−0.0025 (9)0.0044 (10)0.0049 (8)
C40.0758 (16)0.0467 (11)0.0627 (13)−0.0193 (12)−0.0046 (14)−0.0087 (11)
C50.0587 (14)0.0378 (9)0.0625 (13)−0.0042 (10)−0.0083 (12)0.0024 (9)
C60.0704 (15)0.0566 (12)0.0715 (15)−0.0128 (12)−0.0217 (12)0.0201 (11)
C70.0496 (13)0.0480 (11)0.0525 (13)−0.0036 (10)−0.0095 (10)0.0048 (10)
C80.0681 (16)0.0550 (12)0.0705 (15)0.0111 (11)0.0186 (13)0.0048 (12)
C90.094 (2)0.0577 (13)0.0710 (17)−0.0028 (15)0.0181 (15)0.0168 (12)
C100.0819 (19)0.0491 (12)0.0814 (18)0.0038 (13)−0.0133 (16)0.0103 (13)
C110.0651 (17)0.0740 (15)0.0948 (19)0.0241 (15)0.0010 (17)−0.0048 (14)
C120.0568 (15)0.0833 (15)0.0668 (15)−0.0018 (15)0.0091 (13)0.0148 (12)

Geometric parameters (Å, °)

S1—C31.7495 (17)C6—C71.506 (3)
S1—C61.808 (2)C6—H6A0.9700
N1—C31.338 (2)C6—H6B0.9700
N1—C41.350 (3)C7—C81.366 (3)
N2—C41.322 (3)C7—C121.374 (3)
N2—C11.334 (2)C8—C91.376 (3)
N3—C51.358 (2)C8—H80.9300
N3—C11.362 (3)C9—C101.352 (4)
N3—H3N0.894 (19)C9—H90.9300
N4—C51.306 (2)C10—C111.357 (4)
N4—C21.380 (2)C10—H100.9300
C1—C21.392 (2)C11—C121.383 (3)
C2—C31.385 (3)C11—H110.9300
C4—H40.9300C12—H120.9300
C5—H50.9300
C3—S1—C6101.51 (10)C7—C6—H6A109.8
C3—N1—C4116.80 (18)S1—C6—H6A109.8
C4—N2—C1111.39 (16)C7—C6—H6B109.8
C5—N3—C1106.18 (16)S1—C6—H6B109.8
C5—N3—H3N128.6 (13)H6A—C6—H6B108.2
C1—N3—H3N124.8 (14)C8—C7—C12117.73 (19)
C5—N4—C2104.28 (15)C8—C7—C6121.1 (2)
N2—C1—N3128.28 (17)C12—C7—C6121.2 (2)
N2—C1—C2125.9 (2)C7—C8—C9121.6 (2)
N3—C1—C2105.86 (16)C7—C8—H8119.2
N4—C2—C3133.49 (16)C9—C8—H8119.2
N4—C2—C1109.82 (18)C10—C9—C8119.9 (2)
C3—C2—C1116.67 (18)C10—C9—H9120.1
N1—C3—C2119.75 (16)C8—C9—H9120.1
N1—C3—S1121.40 (16)C9—C10—C11120.0 (2)
C2—C3—S1118.85 (14)C9—C10—H10120.0
N2—C4—N1129.52 (19)C11—C10—H10120.0
N2—C4—H4115.2C10—C11—C12120.1 (2)
N1—C4—H4115.2C10—C11—H11120.0
N4—C5—N3113.9 (2)C12—C11—H11120.0
N4—C5—H5123.1C7—C12—C11120.7 (2)
N3—C5—H5123.1C7—C12—H12119.7
C7—C6—S1109.51 (15)C11—C12—H12119.7
C4—N2—C1—N3−179.25 (19)C6—S1—C3—C2173.43 (16)
C4—N2—C1—C2−0.2 (3)C1—N2—C4—N11.0 (3)
C5—N3—C1—N2179.4 (2)C3—N1—C4—N2−0.8 (3)
C5—N3—C1—C20.2 (2)C2—N4—C5—N30.4 (2)
C5—N4—C2—C3−178.5 (2)C1—N3—C5—N4−0.4 (2)
C5—N4—C2—C1−0.2 (2)C3—S1—C6—C7−165.98 (17)
N2—C1—C2—N4−179.20 (19)S1—C6—C7—C877.9 (2)
N3—C1—C2—N40.0 (2)S1—C6—C7—C12−103.9 (2)
N2—C1—C2—C3−0.6 (3)C12—C7—C8—C9−2.2 (4)
N3—C1—C2—C3178.62 (17)C6—C7—C8—C9176.1 (2)
C4—N1—C3—C2−0.2 (3)C7—C8—C9—C101.6 (4)
C4—N1—C3—S1179.49 (15)C8—C9—C10—C110.3 (4)
N4—C2—C3—N1179.0 (2)C9—C10—C11—C12−1.4 (4)
C1—C2—C3—N10.8 (3)C8—C7—C12—C111.0 (4)
N4—C2—C3—S1−0.7 (3)C6—C7—C12—C11−177.3 (2)
C1—C2—C3—S1−178.90 (15)C10—C11—C12—C70.8 (4)
C6—S1—C3—N1−6.23 (19)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N3—H3N···N4i0.894 (19)1.892 (19)2.773 (2)167.9 (18)

Symmetry codes: (i) −x+2, y−1/2, −z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BT5117).

References

  • Bruker (2007). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.
  • Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.
  • Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838.
  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  • Lepage, G. A., Junga, J. G. & Bowman, B. (1964). Cancer Res. 24, 835–840. [PubMed]
  • Mitsuya, H. & Border, S. (1986). Proc. Natl. Acad. Sci. USA, 83 1911–1915. [PubMed]
  • Ragazzi, E., Froldi, G., Santi-Sonein, E., Borea, P. A. & Fassina, G. (1989). Pharmacol Res. 21,707–717. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]

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